The ability of peptides generated from the noncoding strand of DNA to specifically recognize peptides coded by the complementary strand has been observed in several experimental systems (K. L. Bost et al, Proc. Natl. Acad. Sci. USA, 82, 1372 (1985); R. R. Brentani et al, Proc. Natl. Acad. Sci. (USA) 85, 364 (1988); T. S. Elton et al, Proc. Natl. Acad. Sci. USA, 85, 2518 (1988); Y. Shai et al, Biochem. 26, 669 (1987)).
Although the exact chemical nature of the interaction is still not well defined, it appears as if the recognition pattern of the sense and anti-sense peptides involves multi-site interactions between complementary amino acids along the sequence (Y. Shai et al, Biochem. 26, 669 (1987)). The recognition seems to occur independently of strict spatial conformation, but it may be dependent on the hydropathic profiles of the peptide (Y. Shai et al, Biochem. 26, 669 (1987); Y. Shai et al, "Protein Structure, Folding and Design 2", D. O. Oxender, ed., Alan R. Liss, New York, N.Y., (1987)).
The concept of sense:anti-sense interactions was derived from the observation that a unique pattern seemed to exist if the consequence of the transcription of complementary strands of DNA in the 5'-3' direction was considered (J. E. Blalock et al, Biochem. Biophys. Res. Comm. 121, 202 (1984).
It was noted that
1) the codons for hydrophilic amino acids on one strand are generally complemented by codons for hydrophobic amino acids on the other strand and vice versa. PA1 2) The average tendency for "uncharged" (slightly hydrophilic) amino acids was to be complemented by codons for "uncharged" amino acids. PA1 (1) designing an anti-peptide sequence having high affinity and specificity for a target peptide or fragment thereof contained in the polypeptide by the computer operated method described above; PA1 (2) synthesizing an anti-polypeptide comprising the anti-peptide sequence; PA1 (3) contacting said anti-polypeptide with a sample comprising the target polypeptide to promote binding therebetween; PA1 (4) separating said polypeptide-bound anti-polypeptide from the remaining components in the sample; and PA1 (5) separating said polypeptide from the anti-polypeptide. PA1 (1) designing an anti-peptide having high affinity and specificity for a target peptide or fragment thereof contained in the polypeptide by the computer operated method described above; PA1 (2) synthesizing an anti-polypeptide comprising the anti-peptide sequence; and PA1 (3) contacting said anti-polypeptide with a sample comprising the target polypeptide to promote binding therebetween, to thereby protect the polypeptide and prevent the proteolysis thereof when placed in contact with a proteolytic enzyme. PA1 (1) designing an anti-peptide sequence having affinity for the target peptide or a fragment thereof by the computer operated method described above; PA1 (2) synthesizing an anti-polypeptide comprising said anti-peptide sequence; PA1 (3) contacting said anti-polypeptide with a sample comprising said second polypeptide to provide binding therebetween to thereby prevent or reduce the binding of said second polypeptide to said first polypeptide in the presence thereof. PA1 (1) designing an anti-peptide sequence having affinity for a target peptide or a fragment thereof contained in the polypeptide by the computer operated method described above; PA1 (2) synthesizing an anti-polypeptide comprising the anti-peptide sequence; PA1 (3) contacting said anti-polypeptide with a sample comprising the target polypeptide to promote binding therebetween. PA1 (1) designing an anti-peptide sequence having affinity for a target peptide or a fragment thereof contained in the polypeptide by the computer operated method described above; PA1 (2) synthesizing an anti-polypeptide comprising the anti-peptide sequence; PA1 (3) contacting said anti-polypeptide with a sample comprising the target polypeptide to promote binding; and PA1 (4) determining the presence of said polypeptide-bound antipolypeptide. PA1 (1) designing an anti-peptide sequence having affinity for a target peptide or a fragment thereof contained in the polypeptide by the computer operated method described above; PA1 (2) synthesizing an anti-polypeptide comprising the anti-peptide sequence; and PA1 (3) covalently binding at least two molecules of said anti-polypeptide to obtain said macromolecule.
(J. E. Blalock et al, Biochem. Biophys. Res. C.mm., 121, 202 (1984).
The hydropathic values used to deduce these patterns were originally derived to predict protein domains in which each amino acid is assigned a numerical score ranging from +4.5 (very hydrophobic) to -4.5 (very hydrophilic) (J. Kyte et al, J. Mol. Biol. 157, 105 (1982).
The practical applications of sense anti-sense interactions have so far been limited to a few well defined systems for which DNA sequence information is available. The most frequent use has been in receptor purification where antibodies to anti-sense peptides were applied to purify the receptors for corLicotropin (ACTH), fibronectin and angrotensin II (K. L. Bost et al, Proc. Natl. Acad. Sci. (USA) 82, 1372 (1985); (R.R. Brentani et al, Proc. Natl. Acad. Sci. USA, 85, 364 (1988); T. S. Elton et al, Proc. Natl. Acad. Sci. USA, 85, 2518 (1988)). In addition, sense anti-sense interactions have been used to study other systems including the S-peptide, Arg.sup.8 -vasopressin, and neurophysin II (Y. Shai et al, Biochem 26, 669 (1987); G. Fassina et al, J. Cell Biochem , 35, 9 (1987)).
The generation of peptides with recognition properties towards the target peptide based on the ribonucleic acid (RNA) sequence coding for the target peptide was described by Bost, Smith and Blalock, supra. The sequences of these anti-sense peptides are deduced from the non-coding DNA strand which is complementary to the RNA segment encoding a target peptide. An essential requirement for the practice of this prior art method is the knowledge of the nucleic acid sequence encoding the target peptide. This method was later on successfully applied to other systems, thereby permitting the isolation of various target peptides or proteins. In some cases the method also aided in the identification of the receptor protein for the target peptide using antibodies raised against the anti-sense peptide (see, Brentani et al, supra; Elton et al, supra). However, the requirement that the DNA sequence encoding the target peptide be known is a significant drawback which prevents the more extensive use of this method.
Accordingly, there is still a need for a simpler and more efficient method of designing anti-peptides capable of displaying high affinity and specificity for a target peptide or fragments thereof which can be obtained in the absence of information on the ribonucleic acid (RNA) and/or deoxyribonucleic acid (DNA) sequences encoding the target peptide.